The effects of signalment, diet, geographic location, season, and colitis associated with antimicrobial use or Salmonella infection on the fecal microbiome of horses

BACKGROUND: The fecal microbiome of healthy horses may be influenced by signalment, diet, environmental factors, and disease. OBJECTIVES: To assess the effects of age, breed, sex, geographic location, season, diet, and colitis caused by antibiotic use (antimicrobial‐associated diarrhea [AAD]) and Salmonella infection on fecal microbiota. ANIMALS: Healthy horses (n = 80) were sampled from nonhospital environments across multiple geographical locations in the United States. Horses with AAD (n = 14) were defined as those that developed diarrhea secondary to antimicrobial use. Horses with Salmonella infection (n = 12) were presented with spontaneous onset of colitis and subsequently tested positive on Salmonella quantitative polymerase chain reaction. All horses were >1 year of age and stratified by a dietary scale that included forages (pasture and hay) and concentrates grouped by percentage of fiber and amount. METHODS: Illumina sequencing of 16S rRNA genes was performed on fecal DNA. RESULTS: Healthy horses fed higher amounts of grain clustered separately from those fed lower amounts of grain (analysis of similarities [ANOSIM], R = 0.356‐0.385, Q = 0.002). Horses with AAD and Salmonella had decreased richness and evenness compared to healthy horses (P < .05). Univariable analysis of the 3 groups identified increases in Bacteroidetes (Q = 0.002) and Protebacteria (Q = 0.001) and decreases in Verrucomicrobia (Q = 0.001) in AAD horses whereas Salmonella horses had less Firmicutes (Q = 0.001) when compared to healthy horses. CONCLUSIONS AND CLINICAL IMPORTANCE: Although the amount of grain in the diet had some impact on the fecal microbiome, colitis had a significantly larger influence. Horses with ADD have a more severe dysbiosis than do horses with Salmonella.